transforming the axiomisation of ontologies: the ontology pre-processor language
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Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Ontology Pre-Processor Language (OPPL)http://oppl.sourceforge.net/
Mikel Egaña (mikel.eganaaranguren@cs.man.ac.uk)Robert Stevens (robert.stevens@manchester.ac.uk)
Bio-Health Informatics Group (BHIG), University of Manchester
Erick Antezana (erant@psb.ugent.be)Department of Plant Systems Biology, VIB, Gent, Belgium
Department of Molecular Genetics, Ghent University, Gent, Belgium
OWLED 2008 DC
March 24, 2008
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Introduction to OPPL
“Macro” language for manipulating content of OWL ontologies
Motivation: authors’ needs when creating/maintainingbio-ontologies (Use cases)
Nearly API-level functionality with minimum programming/OWLknowledge
Manchester OWL Syntax + SELECT, ADD, REMOVE
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Introduction to OPPL
“Macro” language for manipulating content of OWL ontologies
Motivation: authors’ needs when creating/maintainingbio-ontologies (Use cases)
Nearly API-level functionality with minimum programming/OWLknowledge
Manchester OWL Syntax + SELECT, ADD, REMOVE
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Introduction to OPPL
“Macro” language for manipulating content of OWL ontologies
Motivation: authors’ needs when creating/maintainingbio-ontologies (Use cases)
Nearly API-level functionality with minimum programming/OWLknowledge
Manchester OWL Syntax + SELECT, ADD, REMOVE
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Introduction to OPPL
“Macro” language for manipulating content of OWL ontologies
Motivation: authors’ needs when creating/maintainingbio-ontologies (Use cases)
Nearly API-level functionality with minimum programming/OWLknowledge
Manchester OWL Syntax + SELECT, ADD, REMOVE
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction
SELECT Class: admin;ADD label "office admin";OPPL statement OPPL statement
OPPL instruction
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
ADD Class: undergraduate;
REMOVE Class: undergraduate;
SELECT equivalentTo participates_in only(intellectual_dinner and party);ADD label "professor";REMOVE subClassOf lives_on only (not campus);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
ADD Class: undergraduate;
REMOVE Class: undergraduate;
SELECT equivalentTo participates_in only(intellectual_dinner and party);ADD label "professor";REMOVE subClassOf lives_on only (not campus);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
ADD Class: undergraduate;
REMOVE Class: undergraduate;
SELECT equivalentTo participates_in only(intellectual_dinner and party);ADD label "professor";REMOVE subClassOf lives_on only (not campus);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
SELECT subClassOf MoleOfSalt;ADD subClassOf hasDensity value 0.0;
SELECT inverse participates_in;ADD range student;
ADD Class: professor;ADD label "staff";ADD equivalentTo participates_in only(intellectual_dinner and party);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
SELECT subClassOf MoleOfSalt;ADD subClassOf hasDensity value 0.0;
SELECT inverse participates_in;ADD range student;
ADD Class: professor;ADD label "staff";ADD equivalentTo participates_in only(intellectual_dinner and party);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
SELECT subClassOf MoleOfSalt;ADD subClassOf hasDensity value 0.0;
SELECT inverse participates_in;ADD range student;
ADD Class: professor;ADD label "staff";ADD equivalentTo participates_in only(intellectual_dinner and party);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
disjointWith, differentFrom, sameAs, type,descendantOf, ancestorOf, subPropertyOf, ...
http://oppl.sourceforge.net/test.oppl
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL instruction examples
disjointWith, differentFrom, sameAs, type,descendantOf, ancestorOf, subPropertyOf, ...
http://oppl.sourceforge.net/test.oppl
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL extra instructions
SELECT_PRIMITIVE descendantOf student;
SELECT_DEFINED descendantOf student;
SELECT descendantOf person;ADD disjointWithSiblings;
SELECT assertedSubClassOf participates_in somesport;
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL extra instructions
SELECT_PRIMITIVE descendantOf student;
SELECT_DEFINED descendantOf student;
SELECT descendantOf person;ADD disjointWithSiblings;
SELECT assertedSubClassOf participates_in somesport;
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL instructionOPPL instruction examplesOPPL extra instructions
OPPL extra instructions
SELECT_PRIMITIVE descendantOf student;
SELECT_DEFINED descendantOf student;
SELECT descendantOf person;ADD disjointWithSiblings;
SELECT assertedSubClassOf participates_in somesport;
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
OPPL software
http://oppl.sourceforge.net/
OPPLInstructionManagerJava library for processing OPPL instructions (LGPL)OWL API, Pellet, FaCT++, DIG
OPPL reference implementation: OPPL instructions in flat filejava -jar oppl.jarpellet ins.oppl ont.owl new_ont.owl
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
OPPL software
http://oppl.sourceforge.net/
OPPLInstructionManagerJava library for processing OPPL instructions (LGPL)OWL API, Pellet, FaCT++, DIG
OPPL reference implementation: OPPL instructions in flat filejava -jar oppl.jarpellet ins.oppl ont.owl new_ont.owl
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
OPPL software
http://oppl.sourceforge.net/
OPPLInstructionManagerJava library for processing OPPL instructions (LGPL)OWL API, Pellet, FaCT++, DIG
OPPL reference implementation: OPPL instructions in flat filejava -jar oppl.jarpellet ins.oppl ont.owl new_ont.owl
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 1: Bio-ontology axiomatic enrichment
Gene Ontology Next Generationhttp://www.gong.manchester.ac.uk/
alanine:sodium symporter activity
—— Axiomatic enrichment based in rdfs:label ——
EquivalentTo: symporter activityand transports only (alanine or sodium)
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 1: Bio-ontology axiomatic enrichment
Gene Ontology Next Generationhttp://www.gong.manchester.ac.uk/
alanine:sodium symporter activity
—— Axiomatic enrichment based in rdfs:label ——
EquivalentTo: symporter activityand transports only (alanine or sodium)
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 1: Bio-ontology axiomatic enrichment
rdfs:label: alanine:sodium symporter activityrdfs:label: glycine:potassium symporter activityrdfs:label: valine:sodium symporter activity...
—— —— —— —— —— —— —— —— ——
SELECT label "(.+):(.+) (symporter activity)";ADD equivalentTo symporter_activity andtransports only (<1> or <2>);
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
http://www.cellcycleontology.org/
Gather knowledge about the cell cycle in 5 ontologies
Ontologies created anew each pipeline execution
Impossible to add new axioms by hand to 5 ontologies:- Axioms overwritten each time the pipeline is executed- Many axioms in different places- Ontologies too big
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
http://www.cellcycleontology.org/
Gather knowledge about the cell cycle in 5 ontologies
Ontologies created anew each pipeline execution
Impossible to add new axioms by hand to 5 ontologies:- Axioms overwritten each time the pipeline is executed- Many axioms in different places- Ontologies too big
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
Add axioms automatically each time the pipeline is executed
Explicit development
Querying capabilities
Flexible development
Ontology Design Patternshttp://odps.sourceforge.net
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
Add axioms automatically each time the pipeline is executed
Explicit development
Querying capabilities
Flexible development
Ontology Design Patternshttp://odps.sourceforge.net
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
Add axioms automatically each time the pipeline is executed
Explicit development
Querying capabilities
Flexible development
Ontology Design Patternshttp://odps.sourceforge.net
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
Add axioms automatically each time the pipeline is executed
Explicit development
Querying capabilities
Flexible development
Ontology Design Patternshttp://odps.sourceforge.net
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
Add axioms automatically each time the pipeline is executed
Explicit development
Querying capabilities
Flexible development
Ontology Design Patternshttp://odps.sourceforge.net
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
OPPL softwareUse case 1: Bio-ontology axiomatic enrichmentUse case 2: Cell Cycle Ontology
Use case 2: Cell Cycle Ontology
# Create object property inmediately_precedes
ADD ObjectProperty: inmediately_precedes;ADD functional;ADD subPropertyOf precedes;ADD inverse inmediately_preceded_by;ADD domainCCO_U0000002;ADD range CCO_U0000002;
# Meiotic cell cycle: G1 -> S -> G2 -> M
SELECT Class: CCO_P0000327;ADD subClassOf inmediately_preceded_by someCCO_P0000325;ADD subClassOf inmediately_precedes some CCO_P0000326;
# Query 1: Proteins acting in the mitotic S phase (At)
ADD Class: query_1;ADD subClassOf query;REMOVE subClassOf Thing;ADD comment "Proteins acting in the mitotic S phase";
SELECT subClassOf participates_in some (CCO_P0000014 or (part_of someCCO_P0000014));ADD subClassOf query_1;
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Future of OPPL
Syntax closer to OWL?ADD Class: professorADD professor subClassOf Thing
Loops, conditional control, subroutines, ...
Variables?SELECT subClassOf part_of some ?x;ADD equivalentTo part_of only ?x;
SET professor label "new label";
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Future of OPPL
Syntax closer to OWL?ADD Class: professorADD professor subClassOf Thing
Loops, conditional control, subroutines, ...
Variables?SELECT subClassOf part_of some ?x;ADD equivalentTo part_of only ?x;
SET professor label "new label";
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Future of OPPL
Syntax closer to OWL?ADD Class: professorADD professor subClassOf Thing
Loops, conditional control, subroutines, ...
Variables?SELECT subClassOf part_of some ?x;ADD equivalentTo part_of only ?x;
SET professor label "new label";
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Future of OPPL
Syntax closer to OWL?ADD Class: professorADD professor subClassOf Thing
Loops, conditional control, subroutines, ...
Variables?SELECT subClassOf part_of some ?x;ADD equivalentTo part_of only ?x;
SET professor label "new label";
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Future of OPPL
Formal grammar
Protégé plugin (autocomplete, syntax validation, logs, ...)
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Future of OPPL
Formal grammar
Protégé plugin (autocomplete, syntax validation, logs, ...)
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
Introduction to OPPLOPPL SyntaxUsing OPPL
Future of OPPL
Acknowledgements
Mikel Egaña: University of Manchester and EPSRC
Erick Antezana: European Science Foundation (ESF) for theactivity entitled Frontiers of Functional Genomics
http://oppl.sourceforge.net/
Mikel Egaña, Robert Stevens, Erick Antezana Ontology Pre-Processor Language
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